SMTL ID : 4zm9.2 (1 other biounit)

Crystal structure of circularly permuted human asparaginase-like protein 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.51 Å

Oligo State

homo-dimer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 6 residues within 4Å: Chain A: L.55, E.56, D.58, F.61, A.63, C.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.61, A:F.61 NA.8: 5 residues within 4Å: Chain A: E.76, D.78, A.94, K.199, R.203 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.94, A:K.199, A:K.199 Water bridges: A:G.205 NA.9: 7 residues within 4Å: Chain A: T.175, T.191, D.206, S.207, T.225, T.226 Ligands: GLY.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:T.225, G.2 NA.10: 6 residues within 4Å: Chain B: L.55, E.56, D.58, F.61, A.63, C.65 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.56, B:F.61, B:A.63

2 x GLY: GLYCINE(Non-covalent)

GLY.2: 13 residues within 4Å: Chain A: T.175, T.193, G.195, I.196, R.203, G.205, D.206, S.207, G.227, G.229, I.232 Ligands: DTT.7, NA.9 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:G.227, A:G.227, A:G.227, A:G.229, G.2 Water bridges: A:S.207 Salt bridges: A:R.203 GLY.11: 11 residues within 4Å: Chain B: T.175, T.193, G.195, I.196, R.203, G.205, D.206, S.207, G.227, G.229 Ligands: FLC.12 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.227, B:G.227, B:G.229 Water bridges: B:D.78, B:S.207 Salt bridges: B:R.203

5 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.3: 8 residues within 4Å: Chain A: S.88, A.89, V.108, M.109, T.112, P.113, H.114 Chain B: K.234 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.89, B:K.234 BME.4: 3 residues within 4Å: Chain A: G.36, R.39, G.316 No protein-ligand interaction detected (PLIP) BME.5: 4 residues within 4Å: Chain A: V.33, G.50, V.53, A.54 No protein-ligand interaction detected (PLIP) BME.6: 5 residues within 4Å: Chain A: G.26, R.29, A.54, L.55, D.58 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.29, A:D.58, A:D.58 BME.13: 3 residues within 4Å: Chain B: R.39, L.314, P.315 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.39, B:R.39

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.7: 7 residues within 4Å: Chain A: G.11, N.62, R.147, T.175, T.226, G.227 Ligands: GLY.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.11, A:N.62, A:T.175

1 x FLC: CITRATE ANION(Non-covalent)

FLC.12: 9 residues within 4Å: Chain B: G.11, N.62, R.147, T.175, G.195, I.196, T.226, G.227 Ligands: GLY.11 7 PLIP interactions: 5 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:G.11, B:N.62, B:T.226, B:G.227, G.11, G.11 Salt bridges: B:R.147

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, W. et al., Intramolecular Cleavage of the hASRGL1 Homodimer Occurs in Two Stages. Biochemistry (2016)

Release Date

2016-02-17

Peptides

Isoaspartyl peptidase/L-asparaginase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Isoaspartyl peptidase/L-asparaginase

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